Topological scoring


Select an input list of genes for upload (plain text file where first column is a list of entrez gene or affimetrix tag id's)


Select a background list (leave it blank for the default set which consists of all network nodes)


Significance level (leave it blank for the default value of 0.05)

Evaluate "topological" significance of nodes in signaling networks using:
Shortest paths among nodes from user's list(default)
Transcription activation paths from drug targets to nodes in user's list
Shortest paths from all nodes to proteins in user's list
Transcriptional activation paths all nodes to proteins in user's list

Please check box if applies (New):
Send the results of the calculation to the following email address:




To read the description of algorithms and the input/output files click here.


Publications:
1. A. Vellaichamy, Z. Dezső, L. JeBailey, A.M. Chinnaiyan, A. Sreekumar, A. I. Nesvizhskii, G.S. Omenn and A. Bugrim: "Topological significance" analysis of gene expression and proteomic profiles from prostate cancer cells reveals key mechanisms of androgen response. PLoS One 2010, 5:e10936 (to access paper click here).

2. Z. Dezső, Y. Nikolsky, J. Miller, D. Cherba, C. Webb and A. Bugrim: Identifying disease-specific genes based on their topological significance in protein networks. BMC Systems Biology 2009, 3:36 (to access paper click here).
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